IN-BIOS9000 – Sequencing technologies, data analysis, and applications
Course description
Course content
The course provides knowledge of sequencing technologies and hands-on experience with the analysis of data from several current sequencing platforms and for various biological and medical applications. Tools, algorithms, and statistical methods for data analysis will be included, as well as data quality assessment and analysis reproducibility. The applications that will be covered may vary from year to year but will typically include de novo whole-genome assembly and variant calling. Other applications like RNA-Seq, ChIP-Seq, or metagenomics could also be covered.
Learning outcome
After completing this course, you will:
- understand the differences, benefits, and drawbacks of the current sequencing technologies, and be able to decide which platform to use in what way for the different applications
- be able to evaluate sequencing data quality and quantity
- know the tools, algorithms, and statistical methods involved in the data analysis
- be able to perform bioinformatics analysis with data tailored towards selected applications
- be able to report on the data analysis in such a way that the methods used and the steps taken are transparent, thus enhancing reproducibility
- be aware of, and know to deal with, the ethical and data-sensitivity issues surrounding sequencing data derived from human subjects
- be able to critically evaluate, validate and judge the results of bioinformatics analysis of sequencing experiments in terms of underlying assumptions, reliability, sensitivity and specificity, and evaluate their value for answering biological questions
Admission to the course
PhD candidates from the University of Oslo should apply for classes and register for examinations through?Studentweb.
If a course has limited intake capacity, priority will be given to PhD candidates who follow an individual education plan where this particular course is included. Some national researchers’ schools may have specific rules for ranking applicants for courses with limited intake capacity.
PhD candidates who have been admitted to another higher education institution must?apply for a position as a visiting student?within a given deadline.
A maximum of 30 students total for IN-BIO5000 and IN-BIO9000 combined.
Ranking:
- PhD candidates who have the course as a part of their approved PhD plan and are associated with the NORBIS research school.
- PhD candidates who have the course as a part of their approved PhD plan.
- Master students at the Faculty of Mathematics and Natural Sciences who have the course approved in their study plan.
- Master students at the Faculty of Mathematics and Natural Sciences.
- Others
Recommended previous knowledge
We? recommend that participants should have a basic understanding of molecular biology as provided by an introductory course in bioinformatics, molecular biology, or genetics. No formal background in computer science is required, however, students must have a basic understanding of the unix shell. Students should take an introductory unix course beforehand if they do not have these skills.
Overlapping courses
- 10 credits overlap with IN-BIOS5000 – Genome sequencing technologies, assembly, variant calling and statistical genomics.
- 10 credits overlap with INF-BIO5121 – High Throughput Sequencing technologies and bioinformatics analysis (continued).
- 10 credits overlap with INF-BIO9121 – High Throughput Sequencing technologies and bioinformatics analysis (continued).
- 10 credits overlap with INF-BIO5120 – High Throughput Sequencing technologies and bioinformatics analysis (continued).
- 10 credits overlap with INF-BIO9120 – High Throughput Sequencing technologies and bioinformatics analysis (continued).
Teaching
This is an intensive course covering six weeks in the autumn semester in even-numbered years.
The course will start with two continuous weeks of full-day lectures and hands-on exercises.
The following four weeks the students will work on a student project and prepare an oral presentation, which forms part of the exam. They will also read and prepare for the final written exam.
At the end of the sixth week the students will present their student work orally and take a written exam.
80% attendance on lectures and exercises is required to be allowed to take the exams.
Examination
There will be a 2-hour written exam, and the project work will be evaluated based on an oral presentation. Both exams must be passed in the same semester. 80% attendance is required to be allowed to take the exams.
Exams are only organized in the same semesters as the course is given.
It will also be counted as one of?your three?attempts to sit the exam for this course if you sit the exam for ?the following course: IN-BIOS5000 – Genome sequencing technologies, assembly, variant calling and statistical genomics, INF-BIO5121 – High Throughput Sequencing technologies and bioinformatics analysis (continued), INF-BIO9121 – High Throughput Sequencing technologies and bioinformatics analysis (continued)
Examination support material
No examination support material is allowed.
Language of examination
The examination text is given in English, and you submit your response in English.
Grading scale
Grades are awarded on a pass/fail scale. Read more about?the grading system.
Resit an examination
Students who can document a valid reason for absence from the regular examination are?offered a postponed examination at the beginning of the next semester. Re-scheduled examinations are not offered to students who withdraw during, or did not pass the original examination.
More about examinations at UiO
- Use of sources and citations
- Special exam arrangements due to individual needs
- Withdrawal from an exam
- Illness at exams / postponed exams
- Explanation of grades and appeals
- Resitting an exam
- Cheating/attempted cheating
You will find further guides and resources at the web page on examinations at UiO.